Pokémon Link: Rise of the Syndicate (REBOOT)
by Waxing Shadow
Summary: When old enemies rear their ugly heads, it's up to a young group of heroes (along with some elite mentorship) to unlock their true potential and put a stop to the evil threatening to engulf their world.
1. Chapter 1: Calm Before the Storm

**Hi, everyone! I'm back with that reboot I promised, so here we go!**

**Disclaimer: Pokémon is the property of its respective owners (all of which are not me). **

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><p><span>Chapter 1: Calm Before the Storm<span>

The first rays of a new dawn had broken through the clouds at the facility simply known as The Field. To simply call this place a prison would in and of itself be a vast understatement-it was more like a fortress. Aside from having the usual fixtures one would expect in a place like this, tons of security features were added. From electrified gates standing about 15 feet in height, to guards and their Pokémon (Mightyena, Primeape, and any other generally threatening or intimidating ones were preferred) patrolling the areas around the clock, this place was heavily guarded to say the least. There was even a device situated at the center of the prison capable of disrupting poké ball functionality, just in case. Why would all this security be in place, one might ask? Simply put, this penitentiary housed the worst of the worst. Grunts, Admins, and Leaders from the most infamous criminal organizations that the world has to offer wound up doing time here after their schemes failed. Knowing all this, neither the guards nor the populace at large were very worried about the possibility of a breakout. After all, they had this place sealed airtight, right? Maybe they should have been…

"Mail call for a mister… Harmonia, Ghetsis," the security guard called, holding a medium-sized package.

"Over here, fool!"

The guard grumbled something unintelligible and walked over to the prisoner. "Yeah, got a package for you, bright eyes."

Getting a closer look at the elder Harmonia would likely evoke a feeling of disgust. The man formerly known as the cruel, manipulative leader of Team Plasma now looked as twisted physically as he was mentally; he had grayish-green unkempt hair that went down to his hips, a large, scraggly beard, and perhaps most shocking of all, no right arm to speak of. To top off this look, his face seemed to be perpetually twisted into a mixture between a growl and a scowl.

Before the guard handed it over though, he followed standard procedure and radioed a package inspector. After about five minutes, the inspector arrived and got to work.

"Let's see here…a whistle…an MP3 player…a blank CD...and… What do we have here?"

The inspector took out two black and white spheres with buttons at their centers. He studied them curiously for a moment before taking a look back at Ghetsis.

"Seriously, man?"

The would-be dictator looked at the inspector innocently. "Even I like to keep the mementos from my days as a trainer."

Both the guard and inspector gave him doubtful looks, but then just shrugged.

"Eh, I guess he might as well keep it," the inspector said to the guard. "It's not like he could actually use the things anyway."

He was right. At the center of the prison lay a device specifically designed to cancel out the type of frequencies that poké balls emit when functioning, effectively rendering them useless. Unfortunately, that meant that any creature unlucky enough to be in these "dead balls" would be in quite the predicament.

The inspector concluded his business, gave the package to Ghetsis, and promptly left. The guard shot one last suspicious look at the decrepit prisoner before also taking his leave.

Ghetsis looked through his package, a twisted smile forming on his face. This was it, the chance he'd been waiting for all this time. He would finally get his revenge on that boy, that girl, and that stupid, defective moron that thought he could talk to pokémon. They would all pay, and he would rule Unova and then some! He just needed to wait until the time was right.

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><p>Meanwhile, Capt. Sonya Watters was wrapping up training with her three houndoom in a special area on the other side of the prison dedicated to such purposes.<p>

"Good job, boys!"

The houndoom at the center responded with an indignant huff while the other two barked in affirmation. This did not go unnoticed. Capt. Watters rolled her eyes and petted the one in the center.

"Alright, fine. Good job, boys…and girl. That okay with you, Sarah?" The dog made the closest face it possibly could to a satisfied smirk.

The young captain smiled. "Ok, then. Why don't you three head off to the mess hall and get a good meal in your bellies?"

Sarah made a cheery-sounding noise and trotted off with the other two tagging along behind her.

Capt. Watters watched them go. Out of all the uncertainty in her life, she knew one thing for sure: she loved those three houndoom more than anything. Things just hadn't been the same since her mother passed away. After it happened, she spent many nights locked in her room, crying. Out of concern for her, one of her friends pulled some strings, and long story short, she found herself at a local orphanage. Ever since she picked out the three Dark/Fire types, she had loved them like they were here own children. She could even tell the differences in their personalities: Sarah was brash but honest. Ray (the one to the left) was quiet, but always willing to help in a pinch. Paulie (the one to the right) was the hardest working of the group, and at times, would fight with Sarah for the spotlight. Now, they, along with her work in The Field, was what she lived for.

As she left to fill out some paperwork, she couldn't shake this odd feeling of foreboding rolling around in the back of her mind.

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><p><strong>I decided to cut the prologue chapter into pieces to make room for a bit more depth. Review if you'd like!<strong>


	2. Chapter 2: The Man With the Dragon

Chapter 2: The Man With the Dragon

Ghetsis's opportunity arose right after breakfast upon returning to his cell. From what he'd heard from the CD he'd gotten from the package, he was supposed to wait until things got more relaxed before springing his trap. Now was that time. Ghetsis blew the whistle, beginning the nightmare that would shake the foundations of the Pokémon World.

A loud pop was audible throughout the prison, followed by the sounds of the guards' pokémon going absolutely crazy. As everyone struggled to recover, Ghetsis took out one of the Ultra Balls and sent out his Hydreigon. The three-headed creature stretched its neck and roared.

"Now! Use Crunch on those bars!" the madman ordered, a maniacal glint in his eye.

The dragon handled the bars while its trainer hopped on its back.

"Get us out of here, and tear apart anyone that gets in your way!"

Hydreigon smashed through the cell's remains and started its rampage, downing any guards foolish enough to try and stop them with a well-aimed Dragon Pulse. The would-be tyrant felt invincible as he continued to wreak havoc on the prison.

Capt. Watters nearly jumped out of her skin when the alarm went off. Upon regaining her composure, she frowned. Her gut instinct was right after all. She ran to find her dogs. Luckily, they were in one piece, but they clearly were in pain, as they were all howling shrilly with tears in their eyes.

"Guys, come on! We've gotta get going!" the captain ordered, both trying to be heard among the chaos and trying to keep the pain she felt for them out of her voice.

Despite their agony, the trio of houndoom managed to nod in affirmation. Sarah lead and the others followed.

The sounds of both prisoners, pokémon, and guards screaming in pain greeted the young woman and her comrades. As she looked at the carnage, she was both bewildered and terrified. She forced herself to keep moving, as she needed to figure out what was going on here. She repeatedly radioed for backup as she was running, her hopes dropping with every second of silence.

When she got to the recreation yard, she saw something she'd never forget: a man flying on a Hydreigon. Fighting her urge to scream, she went into work-mode and got his attention.

"Hey, you! You're under arrest for…" She trailed off as the man turned to face her. She saw no humanity in this man's eyes. He was a monster in human form, as far as she was concerned.

"Oh, well if it isn't a little bug here to stop me! Obviously, you somehow managed to survive. A pity no one's around… or alive to help you."

Capt. Watters was shocked that he could say something so callous… but upon realizing exactly what he'd said, she was filled with unspeakable sorrow and rage. _He _had injured and killed all those people! He had to pay for this!

"You… you… MONSTER!" she screamed, unsure why she was shaking so furiously right then, but not caring.

His response would haunt her memories forever.

"Monster?" He chuckled madly, then continued. "Such a cute little term. Lady, when I'm done here, you'll be calling me _master_! Besides, you've seen nothing yet compared to what's coming. In short, you won't stop me!"

"Yes I will!" the captain shouted, summoning up what courage she had left. "Sarah, Ray, Paulie: attack!"

The dogs pounced at the dragon on their master's command. The dogs launched attack after coordinated attack, frustrating the man and the dragon's attempts to swat them away. Unfortunately, the man got lucky.

"Focus Blast!"

All three houndoom were blasted by the orange spheres of energy. They were thrown to the ground, whimpering in pain.

"No…" the woman trailed off. She ran to her comrades—no, her family in a panic. She didn't even see the Iron Tail attack coming.

Before she could register what was happening, she felt her hand grab onto something heavy and metallic. It was Hydreigon's tail! She turned to the madman with a predatory stare, not really all there herself at this point. Her eyes glowed red for a split second. Her piercing gaze seemed to have a weird effect on the pokémon facing her. It froze in place with electricity arcing around it. It was almost as if…

She left the thought behind as she shouted her next four words:

"GO. AWAY. RIGHT. NOW!"

Another curious result. In response to her booming voice, both the man and dragon were literally blown away. Far away, as the man's screams showed.

After he was gone, she immediately turned her attention to the houndoom. They were all unconscious, and before she could even question what the heck just happened, she joined them in the encroaching darkness.

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><p><strong>This concludes our prologue, ladies and gentlemen! Read and review if you want!<strong>


	3. Chapter 3: Breaking News

**Miss me? Here's your chapter!**

**Disclaimer: I own Pokémon not.**

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><p>Chapter 3: Breaking News<p>

"Hariyama, Force Palm, now!"

At its trainer's orders, the Arm Thrust Pokémon smashed its palm into what had to be the 50th wild Lairon it was competing with, sending its opponent flying with ease. Cassie Evans looked on, pleased, yet exhausted.

"Nice work, Hariyama. We should be ready now," she said. The Fighting-type grunted in acknowledgement as it was recalled to its pokéball.

Like many trainers, Cassie dreamed of conquering the Pokémon League and becoming its newest Champion. She'd trained long and hard for each Gym battle, spending quite a few sleepless nights training with her pokémon. She even doubled her and her team's efforts upon reaching the notorious Victory Road. Deep down though, she knew she was simply distracting herself from something.

The girl walked through the rose garden at the Road's end, taking a second to admire its beauty before heading out of the cave and traveling to the main building. She was not prepared for what she saw next.

Firstly, Nurse Joy and the clerk weren't at their usual stations; they instead were staring at a TV screen in a corner of the room, seemingly transfixed. They didn't seem to notice Cassie come in, so she decided to get their attention.

"Um… Hello?"

She got no response.

"Excuse me, I'd like a little help, please," she said with a bit of force.

Nothing.

Now Cassie was irritated. She needed to heal her pokémon, and she needed quite a bit of rest herself after her long hike. She really didn't have time for this.

Deciding to confront the workers, she walked towards them and whirled around the nurse to talk to her.

"Look, I've been in that cave over there for the past 3 hours, and my pokémon and I are tired, and…"

Cassie's frustrated ranting stopped in its tracks when she realized that Nurse Joy hadn't heard a word she'd said. Not only that, but she seemed to be looking right through her, her eyes glazed over and fear spread throughout her features.

"What's wrong with you guys?" The trainer asked, more than a little unnerved by their behavior. "I'm talking to you."

Both the clerk and nurse remained silent. However, the clerk used the nearby remote to turn the volume up on the TV.

"…live coverage, reporting at The Field Interregional Correctional Facility. For those just tuning in, you can see the chaos behind me as Medivacs and an army of medically trained people and pokémon swarming the ruins of what used to be called "the ultimate prison" by many."

The camera panned out to show a more detailed look, and Cassie immediately wished that it hadn't. The place looked more like a war zone than a prison: rubble stacked on top of debris as the ruined structures stretched on. People and pokémon were strewn around like dolls in a child's playpen, each with various injuries. The medical staff seemed to be swamped, despite their numbers. The camera refocused on the reporter.

"As you can see, the devastation here is immeasurable. Right now, there are about 50 confirmed dead, and the death toll keeps climbing for both people and pokémon as we speak."

Cassie could sense the dread in her voice, and could tell that she would not like what the reporter said next.

"In the last hour, we'd received word that the infamous Unovan terrorist Ghetsis Harmonia along with Sonya Watters, Chief Warden here at the prison, have disappeared along with several others."

Cassie's jaw dropped at this news. She was stunned to hear that both a respected police officer and a raving lunatic could just… vanish.

"Their whereabouts are completely unknown at this time." The reporter gained a pleading edge to her voice. "If you know anything about where they could be, please don't hesitate to call someone. It doesn't matter who. Just… do it."

The fear in her eyes betrayed the neutral demeanor the reporter was trying to keep. She was like a five year-old that was afraid of the dark. Even though she wouldn't willingly show it, what she'd just seen had outright traumatized her. Cassie reacted differently.

She was furious.

_Who could do such a thing?_ That was her only thought as she balled her fists and stared at the TV blankly. She was sure that this wasn't the work of some rogue pokémon, and vowed in that moment that whoever did this would pay by her hand, no matter what.

A bright light snapped her out of her rage-blinded state as she saw her surroundings fade away before her very eyes. She couldn't have ever imagined the adventure she would embark on upon reappearing.


	4. Chapter 4: In a Strange Lab

**Hi everyone! I'm not dead! Anyway, I'm finally back with another chapter. Here you go!**

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><p>Chapter 4: In a Strange Lab<p>

Upon coming back to reality, Cassie realized that her surroundings were quite different. For starters, she was in the same Pokémon Center that she'd watched that news broadcast in. In fact, what she was looking at was a labyrinth of technology, some familiar, some not. It was pretty hard to make sense of exactly where she was, but as she looked around her immediate person, she was startled by the realization that she was in some kind of glass tubing. She looked around from her vantage point to see that the laboratory was pretty much deserted._ Still_,_ knocking's with a try_, she thought as she started banging on the glass. After what felt like five minutes of glass pounding, she seemed to get a response.

Footsteps.

Cassie tensed up, not quite knowing what to expect. A figure began to come into view. It appeared to be a tall, thin man with a light complexion and dark brown hair. He wore a purple turtleneck and tan slacks. What irritated the misplaced girl, though was that oh-so superior grin he had plastered on his face. It's almost as if he knew this would happen. The man's words seem to confirm her suspicions.

"Well, well, well… It's about time you showed up, Cassie."

That got the girl seething.

"Let me out of here. Now," she spat through gritted teeth.

The man chuckled to himself. "I see. You're a fiery one, aren't you?"

"Yes, I am. And unless you want me to immolate you right here, you'd better get me out of this… whatever it is."

Not the least bit intimidated, the man took out some kind of device and hit a button, causing Cassie's glass prison to dissolve around her, giving her fresh air at last.

After about 15 seconds of letting the fresh air invade her lungs, her attention snapped back to her apparent captor. The thoughts were too muddied in her own anger and confusion to bother to question what just happened. The man, though, looked at her as if she was the most harmless little caterpie in the forest.

"You might want to calm down, there. Some of this equipment is very sensitive."

"Does it look like I give a hoot about your 'sensitive technology'? You are going to tell me what the heck's going on right here, right now!" Cassie screamed, now grabbing on to the man's collar.

"You might not want to take that tone with me. I believe you know who I am."

Cassie's temper gave way to a mix of curiosity and yet more confusion as she put the man down and studied his features carefully. Come to think of it, he did look kind of familiar…

That's when it hit her.

This was Bill, the creator of the Pokémon Storage System. He was the reason why trainers can store hundreds of excess Pokémon—all on the web. Not only that, but he had a lot of clout with the Pokémon League, and she wasn't about to risk her license.

"Bill," Cassie mumbled in quiet irritation.

"Nice to see you, too."

"What's going on here?" Cassie asked, now looking more forlorn than angry.

"Don't worry," Bill reassured, his tone now much more sympathetic. "I'll explain everything after your little meet and greet."

"What?"

"Follow me," the programmer instructed evenly, leading the now clueless girl out of the lab and into a series of hallways.

Cassie's thoughts wandered about as her body autonomously dragged her along. First a psychopath breaks out of prison, and now she'd been abducted by a glorified tech geek? She had a feeling she should've stayed in bed today.

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><p><strong>Bill's quite the piece of work, isn't he? Feel free to review. See you soon.<strong>


	5. Chapter 5: Always the Quiet Ones

**We start introducing the team in these next couple of chapters, so I apologize in advance for the lack of action. Either way, enjoy!**

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><p>Chapter 5: Always the Quiet Ones<p>

Bright light overcame Cassie's vision as she was led into a rather large sitting area. As mixed up as she was about the whole situation, she had to admit that the place looked marvelous: the room was lined with furnishings befitting a fancy hotel. Comfy looking couches lined the outer walls, adjoined by glass tables and hand-carved wooden chairs. A flat-screen TV was mounted on a wall at the center of the room. She was so busy taking in the place itself that it took her awhile to notice that she wasn't alone.

Two teenagers, a little boy, and what seemed like a woman in her 20s were in various stages of relaxation/boredom as they did different things. The first teenager, a boy, was busy fiddling with what appeared to be a Pokégear. The second, a girl, gave her a studying look, but smiled afterwards, as if she'd decided that Cassie wasn't a threatening presence. She waved at her, and Cassie waved back rather awkwardly. Turning her attention to the younger boy, he was sleeping peacefully on the couch, drool hanging from his lip. The woman seemed to be staring at the TV, eyes glazed over. Whether she was even conscious was anyone's guess.

"Like the accommodations here?" Bill asked, breaking the silence.

Seeing all of this, she wasn't exactly in a position to say no. "This place looks all well and good, but what are they doing here?"

"These are your teammates," Bill answered. "Be sure to get to know them, because you'll be counting on them—and vice versa—a lot from now on."

Cassie glared at the PC Storage System designer. "That didn't answer my question. In fact, I have a number of questions…"

"…that we'll get to in due time," Bill finished, turning to leave. "For right now, though, just focus on getting to know these people. You might be surprised at what you might learn."

Bill was gone before Cassie could question him further. At a loss as to what to do next, she sat down on the nearest couch and buried her head in her hands. She was both exhausted and stressed: a pretty bad combination, especially for her. It felt like forever before she felt a finger touch her shoulder.

She looked up to see the girl who she'd exchanged waves with earlier standing over her.

"Uh, hello. What do you want?"

Her only answer was a concerned look from the girl.

"Well. What do you want?" Cassie repeated, growing impatient.

The girl, while slightly startled by Cassie's tone, still seemed to be concerned more for her well-being than any possible outbursts. She simply sighed and sat next to Cassie.

Ordinarily, Cassie would've protested this, but she wasn't in the best state of mind to do so. Besides, for some reason she couldn't quite pinpoint, she found the girl's presence quite comforting.

"Okay… so what's up?"

She didn't receive an answer. A period of awkward silence followed. Suddenly, a question that she hadn't even considered came to mind.

"Can you talk?"

The girl shook her head 'no' and took out what seemed to be a mini whiteboard and pen. She wrote on it for a few seconds. She then turned it to Cassie.

"No, I can't talk. Something about an anomaly in my vocal chords. I'm Reese, by the way."

"I'm Cassie. Nice to meet you, I guess."

More writing, then, "Nice to meet you, too. Let me guess: you got plucked out of the middle of whatever you were doing by Bill and wound up here?"

"How did you…"

Reese gestured to the rest of the group. By now, the teenage boy had actually looked up to see what was going on. He smiled and threw up a "peace" sign before turning back to the Pokégear. The younger boy was still dreaming peacefully, seemingly unaware of anything that was going on. The woman had turned to her with a dead look in her eyes and a halfhearted, forced smile.

"Huh. What's her story?" Cassie asked, referring to the woman.

"She's been through a lot. Watch the news lately?"

Cassie immediately thought back to the news broadcast. Come to think of it, she did look kind of familiar… That's when it hit her.

"She's that warden! What was her name?" She snapped her fingers repeatedly as she tried to recall the name. "Oh, yeah. Sonya Watters."

_Oh, man, _she thought, remembering what she'd seen. _No wonder she looks so empty inside. She was one of the only ones to survive The Field's destruction…_

Reese and Cassie exchanged sympathetic looks before the latter spoke up, wanting to change the subject.

"So… any other introductions you want to make while we're here?"

Reese put her marker to her chin, tapping pensively for a second. "I know that guy over there that can't seem to come up for air is Colin."

"Oh," Cassie replied, staring at him longer than she ought to have.

Unfortunately for her, Reese caught on. Cassie looked back at her to see a knowing smirk plastered on the girl's face.

"Don't you say…" Cassie caught herself when she realized who she was talking to. "…er, I mean… Oh, you know what I mean!"

Reese shook her head in amusement as she looked on at her flustered friend's antics. _Maybe this'll be fun after all, _she thought.

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><p><strong>Commentary: I sort of envisioned Reese as a bit of a play on the "silent protagonist" trope that lots of Pokemon games love so much.<strong>


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